stdpopsim
A library of standard population genetic models
Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
30 of 76 committers (39.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.5%) to scientific vocabulary
Keywords from Contributors
genomics
genetics
tskit
trees
msprime
coalescent
bioinformatics
population-genomics
annotation
cryptocurrencies
Last synced: 6 months ago
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JSON representation
Repository
A library of standard population genetic models
Basic Info
Statistics
- Stars: 134
- Watchers: 13
- Forks: 95
- Open Issues: 116
- Releases: 6
Created about 7 years ago
· Last pushed 9 months ago
Metadata Files
Readme
Changelog
License
Code of conduct
README.md
stdpopsim
A community-maintained library of standard population genetic simulation models. Please see the stable documentation for further details. (That's the link to docs for the last stable release, for in-development docs, see this link.)
Click 
to start an interactive Jupyter Notebook and start playing with stdpopsim now!
If you use stdpopsim in your work, please cite our papers:
See here for full citation details.
Owner
- Name: PopSim Consortium
- Login: popsim-consortium
- Kind: organization
- Repositories: 11
- Profile: https://github.com/popsim-consortium
A community-driven effort to standardize population genetics
GitHub Events
Total
- Create event: 41
- Release event: 1
- Issues event: 100
- Watch event: 12
- Delete event: 43
- Member event: 1
- Issue comment event: 488
- Push event: 86
- Pull request review event: 131
- Pull request review comment event: 118
- Pull request event: 222
- Fork event: 9
Last Year
- Create event: 41
- Release event: 1
- Issues event: 100
- Watch event: 12
- Delete event: 43
- Member event: 1
- Issue comment event: 488
- Push event: 86
- Pull request review event: 131
- Pull request review comment event: 118
- Pull request event: 222
- Fork event: 9
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| dependabot[bot] | 4****] | 162 |
| Jerome Kelleher | jk@w****k | 151 |
| Graham Gower | g****r@g****m | 140 |
| peter | p****p@g****m | 74 |
| andrewkern | a****n@u****u | 69 |
| Noah Dukler | n****6@c****u | 31 |
| nspope | n****e@u****u | 25 |
| Georgia Tsambos | g****s@s****u | 14 |
| Maria Izabel Cavassim Alves | i****m@g****m | 13 |
| Peter Fields | p****s@j****g | 11 |
| Andrew Kern | 7****n | 8 |
| Inés Rebollo | 4****o | 8 |
| Aaron Ragsdale | a****e@m****a | 8 |
| Murillo R | m****s@g****m | 8 |
| Ariella Gladstein | a****n@g****m | 7 |
| jgallowa07 | j****7@g****m | 7 |
| Christopher Cole | c****e@w****k | 7 |
| chriscrsmith | c****s@u****u | 6 |
| leonardo_iasi | l****i@e****e | 6 |
| Aaron Ragsdale | a****e@m****u | 6 |
| Ariella Gladstein | a****n@e****u | 6 |
| Aaron Ragsdale | 6 | |
| Ilan Gronau | i****u@i****l | 6 |
| Jedidiah Carlson | j****n@g****m | 5 |
| Arjun Biddanda | a****a@g****m | 5 |
| Vitor Pavinato | v****o | 4 |
| Chris Smith | c****s@c****u | 4 |
| Jeffrey Adrion | j****n@i****u | 4 |
| Anastasia | t****a@g****m | 4 |
| Gregor Gorjanc | g****c@g****m | 4 |
| and 46 more... | ||
Committer Domains (Top 20 + Academic)
well.ox.ac.uk: 2
uoregon.edu: 2
mail.utoronto.ca: 2
email.arizona.edu: 2
brown.edu: 1
berkeley.edu: 1
gmx.de: 1
stanford.edu: 1
indiana.edu: 1
colorado.edu: 1
idc.ac.il: 1
math.arizona.edu: 1
eva.mpg.de: 1
mail.mcgill.ca: 1
jax.org: 1
student.unimelb.edu.au: 1
utexas.edu: 1
wifi-131-179-21-243.host.ucla.edu: 1
columbia.edu: 1
mail.com: 1
node474.oscar.ccv.brown.edu: 1
wifi-131-179-20-57.host.ucla.edu: 1
uw.edu: 1
arizona.edu: 1
wisc.edu: 1
bdi.ox.ac.uk: 1
unibas.ch: 1
talapas-ln1.uoregon.edu: 1
cornell.edu: 1
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 176
- Total pull requests: 327
- Average time to close issues: over 1 year
- Average time to close pull requests: 2 months
- Total issue authors: 39
- Total pull request authors: 28
- Average comments per issue: 3.74
- Average comments per pull request: 3.2
- Merged pull requests: 192
- Bot issues: 0
- Bot pull requests: 126
Past Year
- Issues: 36
- Pull requests: 194
- Average time to close issues: 9 days
- Average time to close pull requests: 7 days
- Issue authors: 14
- Pull request authors: 13
- Average comments per issue: 1.33
- Average comments per pull request: 2.46
- Merged pull requests: 115
- Bot issues: 0
- Bot pull requests: 77
Top Authors
Issue Authors
- petrelharp (60)
- grahamgower (21)
- nspope (20)
- gregorgorjanc (9)
- jeromekelleher (8)
- hyanwong (6)
- igronau (5)
- andrewkern (5)
- chriscrsmith (3)
- peterdfields (3)
- RyanGutenkunst (3)
- daikitag (3)
- mufernando (3)
- sidAvad (2)
- agladstein (2)
Pull Request Authors
- dependabot[bot] (140)
- petrelharp (70)
- nspope (33)
- gregorgorjanc (22)
- andrewkern (21)
- clararehmann (20)
- igronau (8)
- hyanwong (7)
- peterdfields (7)
- grahamgower (7)
- silastittes (6)
- kevinkorfmann (4)
- ornobalam (4)
- chriscrsmith (4)
- xin-huang (3)
Top Labels
Issue Labels
enhancement (29)
Model QC (10)
DFE QC (8)
Species QC (7)
bug (7)
good first issue (5)
docs (4)
Demographic model (2)
Species (1)
help wanted (1)
Pull Request Labels
dependencies (140)
python (21)
docs (2)
Packages
- Total packages: 2
-
Total downloads:
- pypi 7,211 last-month
-
Total dependent packages: 1
(may contain duplicates) -
Total dependent repositories: 13
(may contain duplicates) - Total versions: 10
- Total maintainers: 4
pypi.org: stdpopsim
A library of population genetic simulation models
- Homepage: https://github.com/popsim-consortium/stdpopsim
- Documentation: https://popsim-consortium.github.io/stdpopsim-docs/stable/index.html
- License: GNU GPLv3+
-
Latest release: 0.3.0
published 11 months ago
Rankings
Dependent repos count: 4.7%
Forks count: 4.8%
Stargazers count: 6.9%
Dependent packages count: 7.3%
Average: 8.6%
Downloads: 19.4%
Maintainers (4)
Last synced:
6 months ago
conda-forge.org: stdpopsim
Stdpopsim provides a standard library of population genetic simulations, based around a catalog of species definitions, empirical genetic maps and demograpic models.
- Homepage: http://github.com/popsim-consortium/stdpopsim
- License: GPL-3.0-or-later
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Latest release: 0.2.0
published over 3 years ago
Rankings
Dependent repos count: 17.9%
Forks count: 20.3%
Average: 30.8%
Stargazers count: 33.3%
Dependent packages count: 51.5%
Last synced:
6 months ago
Dependencies
environment.yml
conda
- demesdraw
- matplotlib
- msprime
- numpy
- pandas
- scikit-allel
- slim
requirements/CI/requirements.txt
pypi
- appdirs ==1.4.4
- attrs ==21.4.0
- biopython ==1.79
- codecov ==2.1.12
- coverage ==6.3.3
- demes ==0.2.2
- demesdraw ==0.2.0
- flake8 ==4.0.1
- humanize ==4.2.0
- msprime ==1.2.0
- numpy ==1.21.5
- numpy ==1.22.3
- pandas ==1.3.4
- pyslim ==0.700
- pytest ==7.1.2
- pytest-cov ==3.0.0
- pytest-xdist ==2.4.0
- scikit-allel ==1.3.5
- setuptools-scm ==6.4.2
- sphinx ==4.3.2
- sphinx-argparse ==0.3.1
- sphinx-issues ==3.0.1
- sphinx_rtd_theme ==1.0.0
- sphinxcontrib-programoutput ==0.17
- zarr ==2.11.3
requirements/development.txt
pypi
- appdirs *
- attrs *
- biopython *
- black >=22.1.0
- blacken-docs *
- boto3 *
- codecov *
- coverage *
- daiquiri *
- demes ==0.2.0
- demesdraw ==0.2.0
- flake8 *
- humanize *
- msprime >=1.1.0
- numpy *
- pandas *
- pre-commit *
- pyslim >=0.600
- pytest *
- pytest-cov *
- pytest-xdist *
- scikit-allel *
- setuptools_scm *
- sphinx *
- sphinx-argparse *
- sphinx-issues *
- sphinx_rtd_theme *
- sphinxcontrib-programoutput *
- zarr >=2.4
setup.py
pypi
- appdirs *
- attrs >=19.1.0
- humanize *
- msprime >=1.0.4
- numpy *
- pandas *
- pyslim >=0.600
- zarr *